Bacterial transport in volcanic tuff cores under saturated flow conditions

An antibiotic‐resistant bacterium was tested for transport through volcanic tuff and sandstone cores. Tuff cores were representative of the geology of Rainier Mesa located on the Nevada Test Site (NTS). Rapid bacterial transport occurred in some of the tuff cores and all sandstone cores under the hydraulic heads used (5–500 cm). Hydraulic conductivity of the tuff cores ranged widely, 9.6 × 10^‐5 to 7.2 x 10^‐3 cm h^‐1. A much narrower range was observed for sandstone cores, 1.6 × 10^‐2 to 5.9 X 10^‐2 cm h^‐1, which served as experimental controls. The percentage of the initial bacterial inoculum recovered within 3 pore volumes from tuff and sandstone cores ranged from 9.4 to 54.7% and 0.20 to 2.9%, respectively. Bacterial recovery appeared to be controlled by the structure of the flow paths in rock cores and not by overall hydraulic conductivity. Saturated clay‐infiltrated and unfractured zeolitized tuff cores were impermeable to water flow, and therefore bacterial transport was not detected. Three routes of bacterial transport were discerned in permeable rock cores by comparison of the breakthrough patterns of bacteria and tracer solution (chloride ions) in cores of differing lithologies. In sandstone cores, where water flowed evenly through the matrix, bacteria were transported in a dispersed manner throughout the sandstone, whereas bacteria were transported primarily along preferred flow paths (fractures or macropores) in permeable tuff cores.     

Lithotrophic and Heterotrophic Bacteria in Deep Subsurface Sediments and Their Relation to Sediment Properties

Subsurface sediments obtained from three cores drilled to depths of 260 m below the surface in South Carolina were analyzed for heterotrophic bacteria; N₂‐fixing microaerophiles; and nitrifying, sulfur‐oxidizing, and H₂‐oxidizing lithotrophic bacteria. In addition, pore waters were extracted for chemical analysis of inorganic nitrogen species, sulfate, dissolved organic carbon, pH, and Eh. Autotroph populations were generally less than 10³ most probable number (MPN) g^‐1 dry sediment with sulfur‐oxidizing bacteria, detected in 60% of the sediment samples, being the most frequently encountered group. Nitrifying bacteria were detected mainly in sediments from one borehole (P28), and their populations in those sediments were correlated with pore‐water ammonium concentrations. Populations of heterotrophic bacteria in 60% of the sediments were greater than 10⁶ colony forming units (CFU) g^‐1 dry sediment and were typically lower in sediments of high clay content and low pH. Microaerophilic N₂‐fixing bacteria were cultured from >50% and bacteria capable of growth on H₂ were cultured from 35% of the subsurface sediments examined. Sediment texture, which controls porosity, water potential, and hydraulic conductivity, appears to be a major factor influencing microbial populations in coastal plain subsurface sediments.     

Distribution of culturable microorganisms in Fennoscandian Shield groundwater

Microbial populations in 16 groundwater samples from six Fennoscandian Shield sites in Finland and Sweden were investigated. The average total cell number was 3.7×10⁵ cells ml⁻¹, and there was no change in the mean of the total cell numbers to a depth of 1390 m. Culture media were designed based on the chemical composition of each groundwater sample and used successfully to culture anaerobic microorganisms from all samples between 65 and 1350 m depth. Between 0.0084 and 14.8% of total cells were cultured from groundwater samples. Sulfate-reducing bacteria, iron-reducing bacteria and heterotrophic acetogenic bacteria were cultured from groundwater sampled at 65–686 m depth in geographically distant sites. Different microbial populations were cultured from deeper, older and more saline groundwater from 863 to 1350 m depth. Principal component analysis of groundwater chemistry data showed that sulfate- and iron-reducing bacteria were not detected in the most saline groundwater. Iron-reducing bacteria and acetogens were cultured from deep groundwater that contained 0.35–3.5 mM sulfate, while methanogens and acetogens were cultured from deep sulfate-depleted groundwater. In one borehole from which autotrophic methanogens were cultured, dissolved inorganic carbon was enriched in ¹³C compared to other Fennoscandian Shield groundwater samples, suggesting that autotrophs were active. It can be concluded that a diverse microbial community is present from the surface to over 1300 m depth in the Fennoscandian Shield.     

Hydrogeologic parameters affecting vadose‐zone microbial distributions

Abstract

The vadose zone and its contaminant‐attenuating processes are physically interposed between surface contamination and groundwater supplies. Given the potential role of microorganisms in mediating vadose‐zone chemical processes, it is vital to understand vadose microbial distributions and factors controlling those distributions. Vadose and shallow saturated zone sediments obtained from cores drilled to approximately 8 m below the surface at two hydrogeologically contrasting sites, named Dalmeny and Washington State University (WSU), were examined for culturable heterotrophic bacteria, total organic carbon (TOC), and sediment texture. Pore‐water elutions were analyzed for dissolved organic carbon, sulfate, and inorganic nitrogen species. Numbers of cultured bacteria (10³‐10⁷ g^?1) generally decreased with depth at both sites. The TOC decreased uniformly with depth at WSU where soil processes are the sole carbon source; at Dalmeny, where both soil and kerogen carbon are present, TOC was higher and relatively constant with depth. Numbers of distinct colony types at Dalmeny did not decline below the solum. Bacteria at Dalmeny were more numerous, exhibited greater numbers of colony types, and were metabolically more flexible than those at WSU. The smooth decline of numbers with depth at WSU paralleled and may be caused by the TOC decline with distance from a solum source. Sediment permeability and pore‐water flux did not control bulk populations as suggested in previous studies; this may be explained by bacterial residence on fracture surfaces in low‐permeability materials. Psychrotolerant organisms did not appear to be as abundant as mean ambient temperatures might suggest.     

A new occurrence of ambient inclusion trails from the ~1900‐million‐year‐old Gunflint Formation,Ontario: nanocharacterization and testing of potential formation mechanisms

Ambient inclusion trails (AITs) are tubular microstructures thought to form when a microscopic mineral crystal is propelled through a fine‐grained rock matrix. Here, we report a new occurrence of AITs from a fossilized microbial mat within the 1878‐Ma Gunflint Formation, at Current River, Ontario. The AITs are 1–15 μm in diameter, have pyrite as the propelled crystal, are infilled with chlorite and have been propelled through a microquartz (chert) or chlorite matrix. AITs most commonly originate at the boundary between pyrite‐ and chlorite‐rich laminae and chert‐filled fenestrae, with pyrite crystals propelled into the fenestrae. A subset of AITs originate within the fenestrae, rooted either within the chert or within patches of chlorite. Sulphur isotope data (³⁴S/³²S) obtained in situ from AIT pyrite have a δ³⁴S of ?8.5 to +8.0 ‰, indicating a maximum of ~30 ‰ fractionation from Palaeoproterozoic seawater sulphate (δ³⁴S ≈ +20 ‰). Organic carbon is common both at the outer margins of the fenestrae and in patches of chlorite where most AITs originate, and can be found in smaller quantities further along some AITs towards the terminal pyrite grain. We infer that pyrite crystals now found within the AITs formed via the action of heterotrophic sulphate‐reducing bacteria during early diagenesis within the microbial mat, as pore waters were becoming depleted in seawater sulphate. Gases derived from this process such as CO₂ and H₂S were partially trapped within the microbial mat, helping produce birds‐eye fenestrae, while rapid microquartz precipitation closed porosity. We propose that propulsion of the pyrite crystals to form AITs was driven by two complementary mechanisms during burial and low‐grade metamorphism: firstly, thermal decomposition of residual organic material providing CO₂, and potentially CH₄, as propulsive gases, plus organic acids to locally dissolve the microquartz matrix; and secondly, reactions involving clay minerals that potentially led to enhanced quartz solubility, plus increases in fluid and/or gas pressure during chlorite formation, with chlorite then infilling the AITs. This latter mechanism is novel and represents a possible way to generate AITs in environments lacking organic material.     

Microbiological investigations of high-temperature horizons of the Kongdian petroleum reservoir in connection with field trial of a biotechnology for enhancement of oil recovery

The physicochemical conditions and microbiological characteristics of the formation waters of the Kongdian oilfield of the Dagang oilfield (China) were studied. It was demonstrated that this oilfield is a high-temperature ecosystem with formation waters characterized by low mineralization. The concentrations of nitrogen and phosphorus compounds, as well as of electron acceptors, are low. Oil and oil gas are the main organic matter sources. The oilfield is exploited with water-flooding. The oil stratum was inhabited mostly by anaerobic thermophilic microorganisms, including fermentative (10²–10⁵ cells/ml), sulfate-reducing (0–10² cells/ml), and methanogenic (0–10³ cells/ml) microorganisms. Aerobic bacteria were detected mainly in the near-bottom zone of injection wells. The rate of sulfate reduction varied from 0.002 to 18.940 μg S^2? l^?1 day^?1 and the rate of methanogenesis from 0.012 to 16.235 μg CH₄ l^?1 day^?1. Microorganisms with great biotechnological potential inhabited the oilfield. Aerobic thermophilic bacteria were capable of oxidizing oil with formation of biomass, the products of partial oxidation of oil (volatile acids), and surfactants. During growth on the culture liquid of oil-oxidizing bacteria, methanogenic communities produced methane and carbon dioxide, which also had oil-releasing capabilities. Using various labeled tracers, the primary filtration flows of injected solutions at the test site were studied. Our comprehensive investigations allowed us to conclude that the method for microbial enhancement of oil recovery based on the activation of the stratal microflora can be applied in the Kongdian oilfield.     

南海Formosa冷泉区沉积物微生物多样性与分布规律研究

【目的】当前对全球冷泉生态系统微生物生态学研究显示，冷泉生态系统中主要微生物类群为参与甲烷代谢的微生物，它们的分布差异与所处冷泉区生物地球化学环境密切相关。但在冷泉区内也存在环境因子截然不同的生境，尚缺乏比较冷泉区内小尺度生境间微生物多样性和分布规律的研究。本研究旨在分析南海Formosa冷泉区内不同生境间微生物多样性差异，完善和理解不同环境因子对冷泉内微生物群落结构的影响。【方法】对采集自南海Formosa冷泉区不同生境(黑色菌席区、白色菌席区和碳酸盐岩区)沉积物样本中古菌和细菌16S rRNA基因进行测序，结合环境因子，比较微生物多样性差异，分析环境因子对微生物分布的影响。【结果】发现在Formosa冷泉内的不同生境中，甲烷厌氧氧化古菌(anaerobic methanotrophic archaea,ANME)是主要古菌类群，占古菌总体相对丰度超过70%；在菌席区ANME-1b和ANME-2a/b是主要ANME亚群，碳酸盐岩区则是ANME-1b。硫酸盐还原菌(sulfate-reducing bacteria,SRB)和硫氧化菌(sulfur-oxidizing bacteria...     

Microbial communities associated with phosphogenic sediments and phosphoclast‐associated DNA of the Benguela upwelling system

The processes that lead to the precipitation of authigenic calcium phosphate minerals in certain marine pore waters remain poorly understood. Phosphogenesis occurs in sediments beneath some oceanic upwelling zones that harbor polyphosphate‐accumulating bacteria. These bacteria are believed to concentrate phosphate in sediment pore waters, creating supersaturated conditions with respect to apatite precursors. However, the relationship between microbes and phosphorite formation is not fully resolved. To further study this association, we examined microbial community data generated from two sources: sediment cores recovered from the shelf of the Benguela upwelling region where phosphorites are currently forming, and DNA preserved within phosphoclasts recovered from a phosphorite deposit along the Benguela shelf. iTag and clone library sequencing of the 16S rRNA gene showed that many of our sediment‐hosted communities shared large numbers of phylotypes with one another, and that the same metabolic guilds were represented at localities across the shelf. Sulfate‐reducing bacteria and sulfur‐oxidizing bacteria were particularly abundant in our datasets, as were phylotypes that are known to carry out nitrification and the anaerobic oxidation of ammonium. The DNA extracted from phosphoclasts contained the signature of a distinct microbial community from those observed in the modern sediments. While some aspects of the modern and phosphoclast communities were similar, we observed both an enrichment of certain common microbial classes found in the modern phosphogenic sediments and a relative depletion of others. The phosphoclast‐associated DNA could represent a relict signature of one or more microbial assemblages that were present when the apatite or its precursors precipitated. While these taxa may or may not have contributed to the precipitation of the apatite that now hosts their genetic remains, several groups represented in the phosphoclast extract dataset have the genetic potential to metabolize polyphosphate, and perhaps modulate phosphate concentrations in pore waters where carbonate fluorapatite (or its precursors) are known to be precipitating.     

Evidence of oxygenic phototrophy in ancient phosphatic stromatolites from the Paleoproterozoic Vindhyan and Aravalli Supergroups,India

Fossil microbiotas are rare in the early rock record, limiting the type of ecological information extractable from ancient microbialites. In the absence of body fossils, emphasis may instead be given to microbially derived features, such as microbialite growth patterns, microbial mat morphologies, and the presence of fossilized gas bubbles in lithified mats. The metabolic affinity of micro‐organisms associated with phosphatization may reveal important clues to the nature and accretion of apatite‐rich microbialites. Stromatolites from the 1.6 Ga Chitrakoot Formation (Semri Group, Vindhyan Supergroup) in central India contain abundant fossilized bubbles interspersed within fine‐grained in situ‐precipitated apatite mats with average δ¹³C_org indicative of carbon fixation by the Calvin cycle. In addition, the mats hold a synsedimentary fossil biota characteristic of cyanobacterial and rhodophyte morphotypes. Phosphatic oncoid cone‐like stromatolites from the Paleoproterozoic Aravalli Supergroup (Jhamarkotra Formation) comprise abundant mineralized bubbles enmeshed within tufted filamentous mat fabrics. Construction of these tufts is considered to be the result of filamentous bacteria gliding within microbial mats, and as fossilized bubbles within pristine mat laminae can be used as a proxy for oxygenic phototrophy, this provides a strong indication for cyanobacterial activity in the Aravalli mounds. We suggest that the activity of oxygenic phototrophs may have been significant for the formation of apatite in both Vindhyan and Aravalli stromatolites, mainly by concentrating phosphate and creating steep diurnal redox gradients within mat pore spaces, promoting apatite precipitation. The presence in the Indian stromatolites of alternating apatite‐carbonate lamina may result from local variations in pH and oxygen levels caused by photosynthesis–respiration in the mats. Altogether, this study presents new insights into the ecology of ancient phosphatic stromatolites and warrants further exploration into the role of oxygen‐producing biotas in the formation of Paleoproterozoic shallow‐basin phosphorites.     

Effect of Sterilization by Dry Heat or Autoclaving on Bacterial Penetration through Berea Sandstone

A study was undertaken to determine why bacteria could penetrate lengths of consolidated sandstone (Berea) faster when the sandstone was sterilized by autoclaving than when dry heat (150°C, 3 h) was used. Changes in permeability, porosity, and pore entrance size of the rock as a result of autoclaving were not sufficient to explain the differences in penetration times observed, but electron dispersion spectroscopy and electron microscopy of the rock revealed changes in mineral composition and clay morphology. Autoclaved cores contained more chloride than dry-heated cores, and the clays of autoclaved cores were aggregated and irregularly shaped. Therefore, the decreases in bacterial penetration rates caused by autoclave sterilization were probably the result of a change in surface charge of the pores of the rock and of a reduction in surface area of clays available for adhesion. The results implied that dry-heat sterilization was preferable to autoclaving when examining biotic and abiotic interactions in a native-state rock model.     

Linking sedimentary sulfur and iron biogeochemistry to growth patterns of a cold‐water coral mound in the Porcupine Basin,S.W. Ireland (IODP Expedition 307)

Challenger Mound, a 150‐m‐high cold‐water coral mound on the eastern flank of the Porcupine Seabight off SW Ireland, was drilled during Expedition 307 of the Integrated Ocean Drilling Program (IODP). Retrieved cores offer unique insight into an archive of Quaternary paleo‐environmental change, long‐term coral mound development, and the diagenetic alteration of these carbonate fabrics over time. To characterize biogeochemical carbon–iron–sulfur transformations in the mound sediments, the contents of dithionite‐ and HCl‐extractable iron phases, iron monosulfide and pyrite, and acid‐extractable calcium, magnesium, manganese, and strontium were determined. Additionally, the stable isotopic compositions of pore‐water sulfate and solid‐phase reduced sulfur compounds were analyzed. Sulfate penetrated through the mound sequence and into the underlying Miocene sediments, where a sulfate–methane transition zone was identified. Small sulfate concentration decreases (<7 mm ) within the top 40 m of the mound suggested slow net rates of present‐day organoclastic sulfate reduction. Increasing δ³⁴S‐sulfate values due to microbial sulfate reduction mirrored the decrease in sulfate concentrations. This process was accompanied by oxygen isotope exchange with water that was indicated by increasing δ¹⁸O‐sulfate values, reaching equilibrium with pore‐water at depth. Below 50 mbsf, sediment intervals with strong ³⁴S‐enriched imprints on chromium‐reducible sulfur (pyrite S), high degree‐of‐pyritization values, and semi‐lithified diagenetic carbonate‐rich layers characterized by poor coral preservation, were observed. These layers provided evidence for the occurrence of enhanced microbial sulfate‐reducing activity in the mound in the past during periods of rapid mound aggradation and subsequent intervals of non‐deposition or erosion when geochemical fronts remained stationary. During these periods, especially during the Early Pleistocene, elevated sulfate reduction rates facilitated the consumption of reducible iron oxide phases, coral dissolution, and the subsequent formation of carbonate cements.     

Phylogenetic diversity and activity of anaerobic microorganisms of high-temperature horizons of the Dagang oil field (P. R. China)

The number of microorganisms of major metabolic groups and the rates of sulfate reduction and methanogenesis processes in the formation waters of the high-temperature horizons of Dagang oil field have been determined. Using cultural methods, it was shown that the microbial community contained aerobic bacteria oxidizing crude oil, anaerobic fermentative bacteria, sulfate-reducing bacteria, and methanogens. Using cultural methods, the possibility of methane production from a mixture of hydrogen and carbon dioxide (H₂ + CO₂) and from acetate was established, and this result was confirmed by radioisotope methods involving NaH¹⁴CO₃ and ¹⁴CH₃COONa. Analysis of enrichment cultures 16S rDNA of methanogens demonstrated that these microorganisms belong to Methanothermobacter sp. (M. thermautotrophicus), which consumes hydrogen and carbon dioxide as basic substrates. The genes of acetate-utilizing bacteria were not revealed. Phylotypes of the representatives of Thermococcus spp. were found among archaeal 16S rDNA. 16S rRNA genes of bacterial clones belong to the orders Thermoanaerobacteriales (Thermoanaerobacter, Thermovenabulum, Thermacetogenium, and Coprothermobacter spp.), Thermotogales, Nitrospirales (Thermodesulfovibrio sp.) and Planctomycetales. 16S rDNA of a bacterium capable of oxidizing acetate in the course of syntrophic growth with H₂-utilizing methanogens was found in high-temperature petroleum reservoirs for the first time. These results provide further insight into the composition of microbial communities of high-temperature petroleum reservoirs, indicating that syntrophic processes play an important part in acetate degradation accompanied by methane production.     

Opening of Bottleneck Pores for the Improvement of Nitrogen Doped Carbon Electrocatalysts

A facile synthesis strategy to control the porosity of ionothermal nitrogen doped carbons is demonstrated. Adenine is used as cheap and biomass based precursor and a mixture of NaCl/ZnCl₂ as combined solvent‐porogen. Variation of the ratio between the two salt influences the pore structure over a wide range. The eutectic mixture leads to micro‐ and mesoporous material with high total pore volume (TPV) of 3.0 cm³ g^?1 and very high surface area of 2900 m² g^?1 essentially rendering the product an “all‐surface‐area” nitrogen doped carbon. Increasing NaCl contents cause a continuous increase of the mesopore size and the formation of additional macropores resulting in a very high maximal TPV of 5.2 cm³ g^?1, showing 2540 m² g^?1 specific surface area using 60 mol% NaCl. Interestingly, the electrocatalytic activity of the samples toward oxygen reduction is strongly affected by the detailed pore structure. The different—however, chemically equivalent—catalysts vary up to 70 mV in their half wave potentials (E _1/2).The sample with optimized pore system shows a high selectivity toward the favored four electron process and an outstanding E _1/2 of ≈880 mV versus reversible hydrogen electrode (RHE), which is one of the best values reported for nitrogen doped carbons so far.     

Jelly-like Microbial Mats over Subsurface Fields of Gas Hydrates at the St. Petersburg Methane Seep (Central Baikal)

Jelly-like microbial mat samples were collected from benthic surfaces at the St. Petersburg methane seep located in Central Baikal. The concentrations of certain ions, specifically chloride, bromide, sulphate, acetate, iron, calcium, and magnesium, were 2–40 times higher in the microbial mats than those in the pore and bottom water. A large number of diatom valves, cyanobacteria, and filamentous, rod-shaped and coccal microorganisms were found in the samples of bacterial mats using light, epifluorescence and scanning microscopy.Comparative analysis of a 16S rRNA gene fragment demonstrated the presence of bacteria and archaea belonging to the following classes and phyla: Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Verrucomicrobia, Cytophaga-Flavobacteria-Bacteroidetes, Cyanobacteria, and Euryarchaeota. The chemical composition and phylogenetic structure of the microbial community showed that the life activity of the mat occurs due to methane and its derivatives involved. Values of δ¹³C for the microbial mats varied from ?73.6‰ to ?65.8‰ and for animals from ?68.9‰ to ?36.6‰. Functional genes of the sequential methane oxidation (pmoA and mxaF) and different species of methanotrophic bacteria inhabiting cold ecosystems were recorded in the total DNA. Like in other psychroactive communities, the destruction of organic substances forming formed as a result of methanotrophy, terminates at the stage of acetate formation in the microbial mats of Lake Baikal (1,400 m depth). Its further transformation is limited by hydrogen content and carried out in the subsurface layers of sediments.     

Microbial activities in deep subsurface environments

Activities of microorganisms residing in terrestrial deep subsurface sediments were examined in 46 sediment samples from three boreholes. Radiolabeled time course experiments assessing in situ microbial activities were initiated within 30 min of core recovery. [1‐C⁴] Acetate incorporation into lipids, [ methyl‐³H] thymidine incorporation into DNA, [2‐¹⁴C]acetate, and [U‐¹⁴C]glucose mineralization in addition to microbial enrichment and enumeration studies were examined in surface and subsurface sediments. Surface soils contained the greatest biomass and activities, followed by the shallow aquifer zones. Water‐saturated subsurface sands exhibited three to four orders of magnitude greater activity and culturable microorganisms than the dense clay zones, which had low permeability. Regardless of depth, sediments that contained more than 20% clays exhibited the lowest activities and culturable microorganisms.     

Methylmercury concentrations and production rates across a trophic gradient in the northern Everglades

Methylmercury (MeHg) concentrations and production rates were examined along with sulfur biogeochemistry in Everglades sediments in March, July and December, 1995, as part of a large, multi-investigator study, the Aquatic Cycling of Mercury in the Everglades (ACME) project. The sites examined constitute a trophic gradient, generated from agricultural runoff, across the Everglades Nutrient Removal (ENR) Area, which is a re-constructed wetland, and Water Conservation Areas (WCA) 2A, 2B and 3 in the northern Everglades. MeHg concentrations and %MeHg (MeHg as a percent of total Hg) were lowest in the more eutrophic areas and highest in the more pristine areas in the south. MeHg concentrations ranged from <0.1 ng gdw^-1 sediment in the ENR to 5 ng gdw^-1 in WCA3 sediments; and MeHg constituted <0.2% of total Hg (Hg_T) in ENR, but up to about 2% in two sites in WCA2B and WCA3. Methylation rates in surficial sediments, estimated using tracer-level injections of²⁰³ Hg(II) into intact sediment cores, ranged from 0 to 0.12 d^-1, or about 1 to 10 ng g^-1 d^-1when the per day values are multiplied by the ambient total Hg concentration. Methylation was generally maximal at or within centimeters of the sediment surface, and was never observed in water overlying cores. The spatial pattern of MeHg production generally matched that of MeHg concentration. The coincident distributions of MeHg and its production suggest that in situ production controls concentration, and that MeHg concentration can be used as an analog for MeHg production. In addition, the spatial pattern of MeHg in Everglades sediments matches that in biota, suggesting that MeHg bioaccumulation may be predominantly a function of the de novo methylation rate in surficial sediments.Sulfate concentrations in surficial pore waters (up to 400 µm), microbial sulfate-reduction rates (up to 800 nm cc^-1 d^-1) and resultant pore water sulfide concentrations (up to 300 µm) at the eutrophic northern sites were all high relative to most freshwater systems. All declined to the south, and sulfate concentrations in WCA2B and in central WCA3 resembled those in oligotrophic lakes (50–100 µm). MeHg concentration and production were inversely related to sulfate reduction rate and pore water sulfide. Control of MeHg production in the northern Everglades appears to mimic that in an estuary, where sulfate concentrations are high and where sulfide produced by microbial sulfate reduction inhibits MeHg production.     

Comparison of Identification Systems for Classification of Bacteria Isolated from Water and Endolithic Habitats within the Deep Subsurface

One water and three rock samples were taken from a mined tunnel system, U12n, in Rainier Mesa at the Nevada Test Site. Endolithic microorganisms were cultured from ashfall tuff, which was crushed and made into slurries with a formulation of artificial pore water, on R2A agar plates. Microbial counts ranged from 10² to 10⁴ viable cells per g (dry weight) of rock sampled. The cultured water sample yielded 10² viable cells per ml. Many of the isolates were very small (<1 μm) when viewed in the rock matrix and remained small even when cultured. Most were gram-negative rods. Individual isolates were profiled by API-NFT strip number, antibiotic and metal resistance patterns, and colony and cellular morphologies. Three identification systems, API-NFT strips, BIOLOG, and MIDI, were compared. Each system identified only a small percentage of the total isolates, and in only seven cases were the isolates identified the same way by more than one system. The same genus was identified in three of these cases, but different species were indicated. The genus Pseudomonas was the most commonly identified. The isolate profiles and the three identification systems demonstrated that water isolates were considerably different from endolithic isolates.     

Microorganisms of the carbonate petroleum reservoir 302 of the Romashkinskoe oilfield and their biotechnological potential

Diversity, geochemical activity, and biotechnological potential of the microorganisms from oil bed 302 of the Romashkinskoe oilfield (Tatarstan, Russia) are reported. The microbial community contained almost no aerobic microorganisms. Sulfate-reducing (10³?10⁶ cells/mL) and fermentative bacteria (10²?10⁵ cells/mL) predominated in the oilfield. Sulfate reduction was the predominant process in formation water with the rates up to 26.6 μg S^2?L/day. The number of methanogens and methanogenesis rate in formation water did not exceed 10⁴ cells/mL and 8.19 μg CH₄ L/day, respectively. Analysis of the 16S rRNA gene clone library revealed the sequences of denitrifying bacteria of the genera Sulfurimonas and Thauera. The oil recovery technique combining the stimulation of fermentative bacteria and suppression of sulfate reducers in the oilfield was proposed for development of the bed 302. Fermentative bacteria could be activated by the traditional method, i.e., injection of molasses and nitrogen and phosphorus mineral salts through the injection wells. Introduction of high concentrations of nitrate will activate the growth of denitrifying bacteria, suppress the growth of sulfidogenic bacteria, and result in decreased sulfide concentration in formation water. The proposed biotechnology is technologically simple and environmentally friendly.     

Growing a gasdermin pore in membranes of pyroptotic cells

Inflammasome‐activated caspase‐1, caspase‐11, caspase‐4, and caspase‐5 cleave GSDMD to unleash its N‐terminal gasdermin‐N domain (GSDMD^Nterm) that perforates the plasma membrane to execute pyroptosis and stimulate inflammation. The mechanism underlying GSDMD^Nterm pore formation is unclear. Mulvihill et al use high‐resolution atomic force microscopy (AFM) to analyze the dynamic pore formation process of GSDMD^Nterm. GSDMD^Nterm protomers are inserted into the lipid membrane to assemble arc‐ or slit‐shaped oligomers that can incorporate additional protomers and grow into large and stable ring‐shaped oligomers to form pores.     

Rock geochemistry induces stress and starvation responses in the bacterial proteome

Interactions between microorganisms and rocks play an important role in Earth system processes. However, little is known about the molecular capabilities microorganisms require to live in rocky environments. Using a quantitative label‐free proteomics approach, we show that a model bacterium (Cupriavidus metallidurans CH34) can use volcanic rock to satisfy some elemental requirements, resulting in increased rates of cell division in both magnesium‐ and iron‐limited media. However, the rocks also introduced multiple new stresses via chemical changes associated with pH, elemental leaching and surface adsorption of nutrients that were reflected in the proteome. For example, the loss of bioavailable phosphorus was observed and resulted in the upregulation of diverse phosphate limitation proteins, which facilitate increase phosphate uptake and scavenging within the cell. Our results revealed that despite the provision of essential elements, rock chemistry drives complex metabolic reorganization within rock‐dwelling organisms, requiring tight regulation of cellular processes at the protein level. This study advances our ability to identify key microbial responses that enable life to persist in rock environments.